Search Results for "unix linux" - Page 2
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Showing 72 open source projects for "unix linux"
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TEES
Turku Event Extraction System
Turku Event Extraction System (TEES) is a free and open source natural language processing system developed for the extraction of events and relations from biomedical text. It is written mostly in Python, and should work in generic Unix/Linux environments. Currently, the TEES source code repository still remains on GitHub at http://jbjorne.github.com/TEES/ where there is also a wiki with more information. -
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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mod_openopc
just plain WORKS
mod_openopc is a full featured implementation of the OpenOPC library for Python. It is cross platform compatible (full Python 2.5 and up). We used to recommend running it on a POSIX platform (Unix / Linux), but thanks to modest efforts since 2014, performance in Windows OS environments is excellent. -
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Distant Speech Recognition
Beamforming and Speech Recognition Toolkit
BTK contains C++ and Python libraries that implement speech processing and microphone array techniques such as speech feature extraction, speech enhancement, speaker tracking, beamforming, dereverberation and echo cancellation algorithms. The Millennium ASR provides C++ and python libraries for automatic speech recognition. The Millennium ASR implements a weighted finite state transducer (WFST) decoder, training and adaptation methods. These toolkits are meant for facilitating research and... -
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DCMLinux - Dicom Linux Distribution
Dicom PACS solution for free.
DCMLinux is a complete PACS system, free of charge. Its core is an Ubuntu 14.04 system fully updated and it contains the DCM4CHEE as its PACS server. In the near future it will contain many other addons such as Weasis, Oviyam, Care2x, etc. Just download the iso, burn it to a CD and boot it up. No need to configure any files of dcm4chee, DCMLinux installer asks for everything it needs to configure a running PACS in minutes. Project Wiki : http://wiki.dcmlinux.org Project Forums:... -
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GMES
GMES is a free Python package for FDTD electromagnetic simulations.
GMES is a free finite-difference time-domain (FDTD) simulation Python package developed at GIST to model photonic devices. Its features include simulation in 1D, 2D, and 3D Cartesian coordinates, distributed memory parallelism on any system supporting the MPI standard, portable to any Unix-like system, variuos dispersive ε(ω) models, CPML absorbing boundaries and/or Bloch-periodic boundary conditions, and arbitrary material and source distributions. GMES officially stands for GIST... -
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD... -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,... -
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PyRate
Bayesian Estimation of Speciation and Extinction from Fossil Data
PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The method was described by D Silvestro, J Schnitzler, LH Liow, A Antonelli, and N Salamin in Systematic Biology (http://sysbio.oxfordjournals.org/content/early/2014/02/08/sysbio.syu006.abstract). *Please download the most up-to-date code from the "PyRate code" tab on this page or from: https://github.com/dsilvestro/PyRate * *An updated manual... -
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ipcvis
Visualize Inter Process Communication
Small python script that can visualize Inter Process Communication on Linux. It can create a graph of TCP and Unix sockets, pipes and also process hierarchy. Short (59 sec) demo visualizing ssh client connecting to ssh server on the same Ubuntu host: http://youtu.be/8XFKwzkexQY Longer (2 min 13 sec) demo visualizing ZoneMinder surveillance solution operation (stopping, starting, enabling and viewing camera): http://youtu.be/kM7klE61Ibk Tested on Ubuntu 14.10 and Debian 7. ... -
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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mwetoolkit
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/ The Multiword Expressions toolkit aids in the automatic identification and extraction of multiword units in running text. These include idioms (kick the bucket), noun compounds (cable car), phrasal verbs (take off, give up), etc. Even though it focuses on multiword expresisons, the framework is quite complete and can also be useful in any corpus-based study in computational linguistics. The mwetoolkit can be... -
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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**(9 march 2016) this project is continued on github : http://jaapkroe.github.io/polypy ** Python script to analyze (shortest-path) rings in structures read from xyz-files. It can be useful for example to identify defects in crystal structures or molecules.
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW....
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openSEQ
NGS compute distro proloaded with pipeline analysis software
Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The... -
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Malware Analysis Network in Taiwan
MAN in Taiwan, MiT
Malware Analysis Network in Taiwan <Man in Taiwan, MiT> Welcome to contact us (TonTon@TWMAN.ORG) if you are interested in collaborating with us. This project is open source and distributed under the GNU General Public License version 3. Please feel free to add to or modify this source and propose changes or new converters. Developer & Copyrighted by : TonTon Hsien-De Huang Prompter: Jazz Yao-Tsung Wang, Figaro Chen-Ho Yang | Logo Desinger:Temaki Guo Community on... -
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RoboComp is a robotics framework providing a set of open-source, distributed, real-time robotic and artificial vision software components and the necessary tools to create and manage them.
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of... -
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FingerID
Metabolite identification via machine learning.
...FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract. Now it supports unix/linux like system. -
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Aelius Brazilian Portuguese POS-Tagger
Python, NLTK-based package for shallow parsing of Brazilian Portuguese
Aelius is an ongoing open source project aiming at developing a suite of Python, NLTK-based modules and interfaces to external freely available tools for shallow parsing of Brazilian Portuguese. It also includes language resources such as language models, sample texts, and gold standards. Presently, Aelius already offers facilities for POS-tagging and chunking corpora and outputting annotations in different formats, such as in XML in the TEI P5 encoding scheme. -
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That project aims at studying and comparing typical airline IT methods, for instance RM-related algorithms. It works from a Unix/Linux/Mac command-line, and exposes basic APIs. It is being developed in C++, with Python wrappers for some components.
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t2t-pipe
automatic alignment pipeline for parallel treebanks
The *Tree-to-Tree (t2t) Alignment Pipe* is a collection of python scripts, co-ordinating the process of automatic alignment of parallel treebanks from plain text files with a single call from a unix command line. Supported Languages: DE, FR, EN -
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WTMParse
Python script to parse Unix-like WTMP files
Python script that was originally intended for use in forensic examinations that parses WTMP files from Unix-like operating systems and generates a CSS-styled HTML report containing login terminal, username, log start date and login time/date in a table. Good for postmortem forensic examinations or as a way of getting "last" like information where you don't have the ability to boot the machine in question but can grab the wtmp.
